The process here is realy quite simple, just take several, say three or five, pictures at each focus setting and average them all together, because the good information should be constant in all frames in one group and the noise will vary between frames the average of the good will be equal to it's original value and that of the noise will be devided by the number of frames.
The function that works this magic is 'Replace Groups, Average' which is on the Stack menu.
To see the effect averageing frames together can have see this example.